Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= curated2:Q3Z295 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 225 bits (573), Expect = 2e-63 Identities = 148/403 (36%), Positives = 209/403 (51%), Gaps = 37/403 (9%) Query: 23 FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEP 82 F R + LWD +G+ +IDFA GIAV GH HP+L +A+ Q KF HT Y P Sbjct: 28 FYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTA--YQIVP 85 Query: 83 V---LRLAKK---LIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136 + LA++ L + + F ++GAEA E A+K+AR AH + + G++AF Sbjct: 86 YASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIAR--AH----TGRPGVIAFAG 139 Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPPDIRHAAY----NDINSASALID---------- 181 FHGRT+ ++ G+ A Y F P P D+ HA Y + I S AL Sbjct: 140 GFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVKGLFKSDIE 199 Query: 182 -DATCAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMH 240 A+I+EP+QGEGG A F++GLR LCD H LLI DEVQ+G GRTG+L+A H Sbjct: 200 AKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEH 259 Query: 241 YGVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELIN 300 Y V PDL+T AK+L GG P+ A+ E G G TY GNPLA A A VL+++ Sbjct: 260 YDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVME 319 Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ-----AKQIS 355 +++ ++ D E L + +EVRG+G ++ G+ K++ Sbjct: 320 EEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQ 379 Query: 356 QEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAA 396 Q A G+++L G GNV+RF L + + + L A A Sbjct: 380 QHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAKA 422 Lambda K H 0.319 0.136 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 497 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 426 Length adjustment: 31 Effective length of query: 375 Effective length of database: 395 Effective search space: 148125 Effective search space used: 148125 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory